biogems.info - gems for bioinformatics

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#	biogem	description	by	version	released	stars	issues	total	7d	90d**)
								downloads	commits
1	bio	Bioinformatics library	BioRuby project	1.5.1	19 months	319	14	177443	0	0
2	biodiversity	Parser of scientific names	Dmitry Mozzherin	3.4.6	6 weeks	25	4	89151	0	5
3	bio samtools	Binder of samtools for Ruby, on the top	Ricardo Ramirez-Gonzalez, Dan MacLean, Raoul J.P. Bonnal	2.6.2	2 months	26	9	64571	0	10
4	bio gem	Biogem is a software generator for Ruby in	Raoul J.P. Bonnal, Pjotr Prins	1.3.6	3 years	15	12	57297	0	0
5	sequenceserver	Blast search made easy!	Anurag Priyam, Ben J Woodcroft, Vivek Rai et al.	1.0.11	9 months	122	48	54878	4	109
6	bio gadget		Shintaro Katayama	0.5.0	14 months	1	1	43380	0	0
7	bio ucsc api	The Ruby ucsc api: accessing the ucsc genome	Hiroyuki Mishima, Jan Aerts	0.6.4	6 months	16	1	39917	0	0
8	entrez	Http requests to entrez e-utilities	Jared Ning	0.5.8.2	2 years	8	1	36223	0	0
9	bio svgenes	Create pretty svg-format images of features, gene models	Dan MacLean	0.4.1	4 years	15	5	34406	0	0
10	biomart	A Ruby api for interacting with biomart services	Darren Oakley	0.2.3	6 years	17	5	31816	0	0
11	bio maf	Maf parser for BioRuby	Clayton Wheeler	1.0.1	5 years	10	36	29070	0	0
12	bio polyploid tools	Tool to work with polyploids, ngs and molecular	Ricardo H. Ramirez-Gonzalez	0.8.4	5 weeks			27848	0	0
13	bio gff3	Gff3 parser for big data	Pjotr Prins	0.9.1	5 years	7	2	27248	0	0
14	bio blastxmlparser	Very fast parallel blast xml to rdf/html/json/yaml/csv transformer	Pjotr Prins	2.0.4	2 years	13	1	26908	0	0
15	bio grid	A biogem to submit jobs on a queue	Francesco Strozzi	0.3.3	5 years	5	...	25731	0	0
16	search biomodel	Interfaces with biomodel search engine	Niall Beard	2.1.6	6 years	1	...	25526	0	0
17	biointerchange	An open source framework for transforming heterogeneous data	Joachim Baran, Kevin B. Cohen, Geraint Duck et al.	1.0.8	3 years	13	3	23420	0	0
18	obo parser	Ruby parsering for obo files	Matt Yoder	0.4.2	6 years	5	...	22387	0	0
19	bio logger	Log4r wrapper with extra features for roles and	Pjotr Prins	1.0.1	6 years	4	2	21965	0	0
20	bio band	Data mining algorithms for jRuby	arrigonialberto86	0.1.11	4 years	16	3	18890	0	0
21	bio table	Swiss army knife of tabulated data; transforming/filtering tab/csv	Pjotr Prins	1.0.0	3 years	10	21	18848	0	0
22	bio alignment	Support for multiple sequence alignments (msa)	Pjotr Prins	0.1.0	6 months	11	5	18667	0	0
23	bio faster	A fast parser for fastq files	Francesco Strozzi	0.4.5	5 years	10	...	17560	0	0
24	bio vcf	Fast multi-purpose multi-threaded vcf parser	Pjotr Prins	0.9.2	2 years	46	9	15705	0	0
25	bio dbla classifier	A tool to classify and manipulate pfemp1 dbl-alpha	George Githinji	0.7.1	5 years			14731	0	0
26	bio bigbio	Low memory sequence emitters	Pjotr Prins	0.1.6	3 years	11	1	14302	0	0
27	bio rocker	Rocker	Luis (Coto) Orellana, Luis M. Rodriguez-R	1.1.12	23 months			14266	0	0
28	bio phyta	Pipeline to remove contaminations from est libraries	Philipp Comans	0.9.4	6 years	2	1	13796	0	0
29	bio signalp	A wrapper for the signal peptide prediction algorith	Ben J Woodcroft	0.3.1	3 years	3	...	13763	0	0
30	bio ngs	Bio-ngs provides a framework for handling ngs data	Francesco Strozzi, Raoul J.P. Bonnal	0.5.2	5 years	29	15	13640	0	0
31	bio fastqc	Ruby parser for fastqc output	Tazro Inutano Ohta	0.10.2	3 months	2	...	13553	0	3
32	scaffolder	Build genome output files	Michael Barton	0.5.0	4 years	7	...	13409	0	0
33	bio basespace sdk	Basespace Ruby sdk is a Ruby based software	Joachim Baran, Raoul Bonnal, Eri Kibukawa et al.	0.1.7	4 years	11	2	13342	0	0
34	nexus parser	A nexus file format (phylogenetic inference) parser in	mjy	1.1.4	6 years	1	...	13259	0	0
35	bio tm hmm	A BioRuby plugin for interaction with the transmembrane	Ben J. Woodcroft	0.2.4	12 months	2	...	13090	0	0
36	bio kmer counter	A biogem for counting small kmers for fingerprinting	Ben J Woodcroft	0.1.2	4 years	4	...	12954	0	0
37	rubyMorphbank	Simple morphbank (http://morphbank.net) services accessor	mjy	0.2.6	6 years	1	...	12151	0	0
38	bio sambamba	Ruby wrapper for sambamba tool	Artem Tarasov	0.0.5	5 years	2	...	11974	0	0
39	genevalidator	Identifying problems with gene predictions	Monica Dragan, Ismail Moghul, Anurag Priyam et al.	1.6.12	23 months	1	...	11781	0	0
40	bio assembly	BioRuby assembly plugin	Chase Miller, Francesco Strozzi	0.1.0	7 years	4	...	11775	0	0
41	eutils	Lightweight Ruby api for ncbi eutils	Joon Lee, aka seouri	0.2.1	4 years	7	1	11568	0	0
42	bio polymarker db batch	Server for polymarker. to be used with cron	Ricardo H. Ramirez-Gonzalez	0.5.1	3 years		...	11298	0	0
43	bio isoelectric point	A BioRuby plugin for calculating the isoelectric point	George Githinji, Pascal Betz	0.1.3	6 years	3	...	11285	0	0
44	bio velvet	Parser to work with file formats used in	Ben J Woodcroft	0.6.0	3 years		...	11272	0	0
45	bio nexml	BioRuby plugin for reading and writing nexml (http://nexml.org)	Rutger Vos, Anurag Priyam	1.1.0	5 years	8	3	11185	0	0
46	taxonifi	A general purpose framework for scripted handling of development/stable	mjy	0.4.0	5 years	2	1	10811	0	0
47	bioportal	Supports linking of models within a ror application	Stuart Owen, Quyen Nguyen	2.2	4 years		...	10382	0	0
48	bio bgzf	Reading/writing bgzf blocks	Artem Tarasov, Clayton Wheeler	0.2.1	5 years	3	...	10274	0	0
49	bio genomic interval	A BioRuby plugin: handling genomic interavals and overlaps	Hiroyuki Mishima	0.1.2	6 years	4	...	9878	0	0
50	bio graphics	Library for visualizing genomic regions	Jan Aerts	1.4	10 years	23	1	9835	0	0
51	bio octopus	Running and parsing of the protein transmembrane domain	Ben J Woodcroft	0.1.1	6 years	1	...	9022	0	0
52	bio cd hit report	Read and manipulate cd-hit clusters	George Githinji	0.1.0	4 years			8745	0	0
53	bio tabix	Ruby binding for samtools tabix	throwern	1.0.1	4 years	5	1	8570	0	0
54	bio bwa	Ruby binding for bwa mapping software	Francesco Strozzi	0.2.2	6 years	4	...	8395	0	0
55	bio fasta retrieve	Retrieve dna sequence from ucsc using given coordinates	Andrei Rozanski	0.0.7	2 years			8384	0	0
56	bio lazyblastxml	A plugin that allows you to parse large	robsyme	0.4.0	6 years	1	...	8103	0	0
57	bio pipengine	A pipeline manager	Francesco Strozzi, Raoul Jean Pierre Bonnal	0.9.7	7 months	18	4	7927	0	0
58	bio pileup iterator	Iterate through a samtools pileup file	Ben J. Woodcroft	0.0.4	5 years	2	...	7914	0	0
59	bio plasmoap	Implementation of the plasmoap algorithm	Ben J Woodcroft	0.1.1	24 months	1	...	7842	0	0
60	goruby	Gene ontology (go) interface for Ruby	Ben J Woodcroft	0.2.0	7 years	12	...	7791	0	0
61	bio velvet underground	Bindings to some internals of the velvet assembler	Ben Woodcroft	0.3.1	20 months		1	7664	0	0
62	ref2bibtex	Pass a full citation, get the bibtex back,	Matt Yoder	0.2.2	4 weeks		1	7529	0	1
63	bio gngm	Next-generation mapping of mutations	Dan MacLean	0.2.1	5 years	2	...	7374	0	0
64	ruby ensembl api	Api to ensembl databases	Jan Aerts, Francesco Strozzi	1.0.1	7 years	40	5	7351	0	0
65	bio commandeer	Dead simple method of running shell commands from	Ben J. Woodcroft	0.4.0	8 months		...	7313	0	0
66	bio statsample timeseries	Timeseries modules for statsample	Ankur Goel, Claudio Bustos	0.2.1	4 years			7207	0	0
67	bio gff3 pltools	Ruby wrapper for the gff3-pltools	Marjan Povolni	0.3.0	5 years	13	19	7188	0	0
68	publisci	Publish scientific results to the semantic web	Will Strinz	0.1.6	3 years	4	16	7181	0	0
69	bio chembl	Chembl rest api client, parser and container	Mitsuteru Nakao	0.1.3	5 years	1	1	7070	0	0
70	bio ucsc util	Ruby binding to the ucsc kent utilities	throwern	0.1.2	5 years	2	...	6998	0	0
71	bio krona	This biogem is built around krona, a flashy	Ben J. Woodcroft	0.2.0	2 years	1	...	6957	0	0
72	bio rdf	Bioinformatics triple-store support	Pjotr Prins	0.0.2	5 years	4	1	6558	0	0
73	bio affy	Parse affymetrix cel/cdf files	Pjotr Prins	0.5.1	6 years	2	1	6527	0	0
74	genevalidatorapp	A web app wrapper for genevalidator	Monica Dragan, Ismail Moghul, Anurag Priyam et al.	1.5.4	19 months	1	...	6394	0	0
75	bio kb illumina	Geneexpression illuminahumanannotation	Raoul J.P. Bonnal	0.1.0	7 years	1	...	6267	0	0
76	bio unichem	BioRuby plugin for unichem rest web service	Mitsuteru Nakao	0.3.0	5 years			6200	0	0
77	bio synreport	Reports whether a nucleotide change results in synonymous	Dan MacLean	0.1.2	4 years		...	6119	0	0
78	bio liftover	Ruby solution for ucsc liftover tool- (ucsc http://genome.ucsc.edu/cgi-bin/hgliftover)	Andrei Rozanski	1.3.0	4 years	1	...	6051	0	0
79	bio core	BioRuby core plugins, most and stable plugins. blastxmlparser,	Raoul J.P. Bonnal	0.0.1	6 years	1	...	5619	0	0
80	bio protparam	A protparam compatible utility for BioRuby	hryk	0.2.0	5 years	2	1	5560	0	0
81	bio wolf psort wrapper	Enables the localisation predictor wolf psort to be	Ben J Woodcroft	0.0.3	6 years	1	...	5425	0	0
82	bio cnls screenscraper	Programmatic interface to the cnls nuclear localisation signal	Ben J. Woodcroft	0.3.0	5 years	2	...	5401	0	0
83	bio hmmer model	Parse pfam hmm definition files	Ben J. Woodcroft	0.0.2	5 years	1	...	4982	0	0
84	bio gag	Bio-gag is a biogem for detecting and correcting	Ben J Woodcroft	0.1.0	5 years	2	...	4861	0	0
85	ncbi blast dbs	Fast download blast databases from ncbi beta	Anurag Priyam	0.0.6	11 months	7	2	4618	0	1
86	bio biostars analytics	Biostars data-mining and statistical analysis	Joachim Baran	0.2.0	4 years			4610	0	0
87	nbio cloudquery	Client for xoopit's cloudquery api	Cameron Walters, nb.io	0.1.5	8 years	5	...	4404	0	0
88	bio locus	Fast storage and comparison of chr+pos(+alt) locations	Pjotr Prins	0.0.7	2 years	2	1	4396	0	0
89	bio sra	A sequence read archive (sra) download script and	Ben J. Woodcroft	0.3.1	2 years	3	...	4246	0	0
90	bio hmmer3 report	Enables parsing of hmmer version 3 reports	Christian Zmasek, Ben J Woodcroft	0.1.0	2 years	2	1	4093	0	0
91	bio gggenome	Gggenome Ruby client	Mitsuteru Nakao	0.2.0	4 years	1	...	3911	0	0
92	bio ensembl rest	Ruby ensembl rest api	Alberto Donizetti	0.2.0	4 years	2	...	3866	0	0
93	rubyBHL	Rubybhl is a simple request/response wrapper for the	Matt Yoder	0.2.1	4 years	6	...	3735	0	0
94	bio statsample glm	Generalized linear models for statsample	Ankur Goel	0.1.1	4 years			3734	0	0
95	nbio csshttprequest	Csshttprequest is cross-domain ajax using css as a	Cameron Walters, Randy Reddig	1.0.3	9 years	90	1	3723	0	0
96	bio express beta diversity	Interface for express beta diversity	Ben J. Woodcroft	0.1.0	4 years		...	3526	0	0
97	bio mummer	Helper methods for reading .delta files	robsyme	0.2.1	3 years		...	3489	0	0
98	bio repeatmasker	Bio-repeatmasker	Andrei Rozanski	0.0.3	4 years		...	3453	0	0
99	bio sge	BioRuby plugin for sun grid engine	Toshiaki Katayama	0.0.0	7 years	4	...	3347	0	0
100	bio ipcress	A programmatic interface to the ipcress in-silico pcr	Ben J Woodcroft	0.1.0	15 months	3	...	3340	0	0
101	bio cigar	A parser for cigar format alignments	Ben J Woodcroft	0.1.0	4 years	4	...	3338	0	0
102	bio hello	Hello world plugin for the BioRuby (just for	Toshiaki Katayama	0.0.0	7 years	3	...	3320	0	0
103	bio restriction enzyme	Digests dna based on restriction enzyme cut patterns	Trevor Wennblom	1.0.0	6 years		1	3265	0	0
104	bio samtools server	Web server for bio-samtools	homonecloco	0.1.2	3 years		...	3240	0	0
105	dna sequence aligner	Does high pairwise alignment of sequencing reads with	John T. Prince	0.0.2	8 years	1	...	3197	0	0
106	bio emboss six frame nucleotide sequences	A method to get the nucleotide sequence of	Ben J Woodcroft	0.1.0	7 years	1	...	3085	0	0
107	bio core ext	BioRuby core ext: plugins which require external library	Raoul J.P. Bonnal, Pjotr Prins	0.0.1	6 years	1	...	3048	0	0
108	bio biolinux	Meta package for biolinux distribution	Raoul J.P. Bonnal	0.1.0	6 years	2	...	3041	0	0
109	bio ensembl	A Ruby api to the ensembl database	Jan Aerts, Francesco Strozzi	1.1.0	6 years	4	...	3008	0	0
110	bio foo	One-line summary of your gem	Toshiaki Katayama	0.0.0	6 years	1	...	2994	0	0
111	bio data restriction enzyme	Restriction enzyme dataset	Sir Richard J. Roberts, Trevor Wennblom	1.109.0	6 years		...	2993	0	0
112	bio dbsnp	Decoding the dbsnp bitfield	Hiroyuki Mishima	0.1.1	6 years	4	...	2968	0	0
113	bio hydropathy	Hydropathy scale for BioRuby	Ben J Woodcroft	0.0.1	6 years	1	...	2941	0	0
114	bio phyloxml	Phyloxml plugin for BioRuby	Diana Jaunzeikare, Clayton Wheeler	0.9.0	5 years	3	1	2927	0	0
115	intermine bio	Biological extensions for the intermine webservice client library	Alex Kalderimis	0.98.1	6 years	1	...	2926	0	0
116	bio exportpred	Wrapper around the exportpred algorithm for predicting p	Ben J Woodcroft	0.0.1	6 years	1	...	2918	0	0
117	bio aliphatic index	A simple biogem that allows computation of the	Ben J Woodcroft	0.0.1	6 years	1	...	2905	0	0
118	bio old biofetch emulator	Emulates as if old BioRuby biofetch alives	Naohisa Goto	1.0.0	22 months		...	2860	0	0
119	bio incanter	Build graph with jRuby	Matteo Picciolini	0.1.0	5 years			2835	0	0
120	bio img metadata	Reads metadata from integrated microbial genomes (img) metadata	Ben J. Woodcroft	0.0.1	5 years		...	2495	0	0
121	bio gfastqc	Aggregate fastqc (quality control for next generation sequencing	Raoul Jean Pierre Bonnal	0.0.4	2 years		...	2390	0	0
122	bio freebayes	The api for freebayes version #{bio::freebayes::extversion}	Natapol Pornputtapong	0.1.6	2 years			2324	0	0
123	bio stockholm	Parse stockholm sequence alignment format	Ben J. Woodcroft	0.0.1	4 years	2	...	2324	0	0
124	bio raxml	Ruby wrapper to run standard-raxml for maximum likelihood	Fernando Izquierdo	0.1.0	4 years		...	2231	0	0
125	bio kseq	Ruby inferface for kseq.h by heng li for	Fedor Gusev	0.0.2	3 years	1	...	2026	0	0
126	bio exominer	Mine publications for gene names	Pjotr Prins	0.0.3	4 years	1	...	1846	0	0
127	bark	A Ruby wrapper on the open tree api beta	Matt Yoder	0.0.2	3 years	1	...	1754	0	0
128	genomichdt	A restful service for sharing genomic data	Joachim Baran, Robert Buels, Michel Dumontier	0.0.1	4 years			1703	0	0
129	bio faidx	Tools to work with fasta files, indexed with	homonecloco	0.0.1	3 years		...	1679	0	0
130	bio blat tools	Tools to manipulate blat files from the command	homonecloco	0.1.0	3 years		...	1643	0	0
131	bio location rdfize	Faldo location output method for bio::location in BioRuby	Joachim Baran, Naohisa Goto	0.0.0	3 years		...	1608	0	0
132	bio picard	Api of picard tool	Natapol Pornputtapong	1.131.5	2 years			1524	0	0
133	bio sparql client	A Ruby wrapper for bio sparql service	Natapol Pornputtapong	0.0.1	2 years			1467	0	0
134	nbio css http request	Csshttprequest is cross-domain ajax using css disabled	Cameron Walters, Randy Reddig	0.1	9 years			1450	0	0
135	bio jaspar	Tools for jaspar motifs in BioRuby	Jessica Lee, Wasserman Lab	0.1.0	2 years		...	1252	0	0
136	bio conduit	A pipeline creator for BioRuby	Natapol Pornputtapong	1.0.0	2 years			1243	0	0
137	bio kallisto	Basic wrapper for the kallistio mapper	homonecloco	0.1.0	2 years	1	...	1228	0	0
138	bio plates	Methods for handling multiwell plate annotations	Steve Pettitt	0.2.0	2 years		...	1066	0	0
139	bio sam mutation	Parsing and mutation calling from sam, cigar and	Stephen Pettitt	0.4.1	2 years		...	1007	0	0
140	bio gemma wrapper	Cache gemma with loco	Pjotr Prins	0.97	8 weeks		...	896	0	1
141	bio biosql	Biosql plugin for BioRuby	BioRuby project	0.0.0	22 months		...	779	0	0
142	bio shell	BioRuby shell: interactive analysis environment for BioRuby	BioRuby project	0.0.0	6 months		...	379	0	0
143	bio executables	BioRuby executables: utilities bundled with BioRuby	BioRuby project	0.0.0	6 months		...	368	0	0
144	bio primer3	pre		pre			...	0	0	0

*) gem downloads (total & last 90 days) from rubygems.org as of 2018-04-09
**) number of commits on GitHub (last 7 days & last 90 days)